read_pars: Read in parameters from an AD Model Builder run
Description
Reads coefficients, standard errors, log-likelihoods, maximum gradients,
correlation and variance-covariance matrices from AD Model Builder output
files
Usage
read_pars(fn, drop_phase = TRUE)
read_psv(fn, names = NULL)
read_rep(fn, names = NULL)
Arguments
fn
(character) Base name of AD Model Builder
drop_phase
(logical) drop negative-phase (fixed) parameters from results?
names
(character) Names of variables
Value
List containing the following elements
- coefficientsparameter estimates
- coeflistparameter estimates in list format, with proper shape (vectors, matrices, etc.)
- seestimated standard errors of coefficients
- logliklog-likelihood
- maxgradmaximum gradient of log-likelihood surface
- corcorrelation matrix
- vcovvariance-covariance matrix
- nparnumber of parameters
- heshessian matrix (only if no vcov matrix)
Warning
The coeflist component is untested for data
structures more complicated than scalars, vectors or matrices (i.e. higher-dimensional or ragged arrays)Details
Given the output from an ADMB run on FOO.tpl, read_pars reads the
files FOO.par (parameters, log-likelihood, max gradient); FOO.std (standard
deviations); FOO.cor (correlations); FOO.rep (report variables);
admodel.hes for hessian; and admodel.cov for
covariance matrix. read_psv reads the output of MCMC runs